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(-) Description

Title :  REFINED CRYSTAL STRUCTURE OF CANAVALIN FROM JACK BEAN
 
Authors :  T. -P. Ko, A. Mcpherson
Date :  25 Nov 99  (Deposition) - 29 Dec 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B,C,M,N,V,W,X,Y
Keywords :  Duplicated Domains Beta Barrel Helical Loop, Plant Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. P. Ko, Y. G. Kuznetsov, A. J. Malkin, J. Day, A. Mcpherson
X-Ray Diffraction And Atomic Force Microscopy Analysis Of Twinned Crystals: Rhombohedral Canavalin.
Acta Crystallogr. , Sect. D V. 57 829 2001
PubMed-ID: 11375502  |  Reference-DOI: 10.1107/S0907444901003791
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CANAVALIN
    Chains: A, B, C
    Fragment: RESIDUES 46-223
    Organ: SEED
    Organism Common: JACK BEAN
    Organism Scientific: CANAVALIA ENSIFORMIS
    Organism Taxid: 3823
    Other Details: LEGUME STORAGE PROTEIN;
LIMITED DIGESTION BY TRYPSIN
    Tissue: COTYLEDON
 
Molecule 2 - CANAVALIN
    Chains: X, V, N
    Fragment: RESIDUES 246-324
    Organ: SEED
    Organism Common: JACK BEAN
    Organism Scientific: CANAVALIA ENSIFORMIS
    Organism Taxid: 3823
    Other Details: LEGUME STORAGE PROTEIN;
LIMITED DIGESTION BY TRYPSIN
    Tissue: COTYLEDON
 
Molecule 3 - CANAVALIN
    Chains: Y, W, M
    Fragment: RESIDUES 331-423
    Organ: SEED
    Organism Common: JACK BEAN
    Organism Scientific: CANAVALIA ENSIFORMIS
    Organism Taxid: 3823
    Other Details: LEGUME STORAGE PROTEIN;
LIMITED DIGESTION BY TRYPSIN
    Tissue: COTYLEDON

 Structural Features

(-) Chains, Units

  123456789
Asymmetric/Biological Unit : ABCMNVWXY

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1PO43Ligand/IonPHOSPHATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE X:294 , HIS X:297 , ASN X:299 , ARG Y:376BINDING SITE FOR RESIDUE PO4 X 1500
2AC2SOFTWAREPHE V:294 , HIS V:297 , ASN V:299 , ARG W:376BINDING SITE FOR RESIDUE PO4 V 2500
3AC3SOFTWAREARG M:376 , PHE N:294 , HIS N:297 , ASN N:299BINDING SITE FOR RESIDUE PO4 N 3500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1DGR)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1DGR)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1DGR)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1DGR)

(-) Exons   (0, 0)

(no "Exon" information available for 1DGR)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:178
 aligned with CANA_CANEN | P50477 from UniProtKB/Swiss-Prot  Length:445

    Alignment length:178
                                    55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215        
           CANA_CANEN    46 NNPYLFRSNKFLTLFKNQHGSLRLLQRFNEDTEKLENLRDYRVLEYCSKPNTLLLPHHSDSDLLVLVLEGQAILVLVNPDGRDTYKLDQGDAIKIQAGTPFYLINPDNNQNLRILKFAITFRRPGTVEDFFLSSTKRLPSYLSAFSKNFLEASYDSPYDEIEQTLLQEEQEGVIVKMP 223
               SCOP domains d1dgra_ A: Seed storage 7S protein                                                                                                                                                 SCOP domains
               CATH domains 1dgrA00 A:46-223 Jelly Rolls                                                                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eehhh.eeeeee...eeeeee......hhhhhhhh.eeeeeeee...eeeeeeee..eeeeeeee..eeeeee....eeeeee...eeeee.....eeeee......eeeeeeee.........eee........hhhhhhhhhhhhhhhh.hhhhhhhhhh.......eee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dgr A  46 NNPYLFRSNKFLTLFKNQHGSLRLLQRFNEDTEKLENLRDYRVLEYCSKPNTLLLPHHSDSDLLVLVLEGQAILVLVNPDGRDTYKLDQGDAIKIQAGTPFYLINPDNNQNLRILKFAITFRRPGTVEDFFLSSTKRLPSYLSAFSKNFLEASYDSPYDEIEQTLLQEEQEGVIVKMP 223
                                    55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215        


Chain B from PDB  Type:PROTEIN  Length:178
 aligned with CANA_CANEN | P50477 from UniProtKB/Swiss-Prot  Length:445

    Alignment length:178
                                    55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215        
           CANA_CANEN    46 NNPYLFRSNKFLTLFKNQHGSLRLLQRFNEDTEKLENLRDYRVLEYCSKPNTLLLPHHSDSDLLVLVLEGQAILVLVNPDGRDTYKLDQGDAIKIQAGTPFYLINPDNNQNLRILKFAITFRRPGTVEDFFLSSTKRLPSYLSAFSKNFLEASYDSPYDEIEQTLLQEEQEGVIVKMP 223
               SCOP domains d1dgrb_ B: Seed storage 7S protein                                                                                                                                                 SCOP domains
               CATH domains 1dgrB00 B:46-223 Jelly Rolls                                                                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eehhh.eeeeeee..eeeeee......hhhhhhhh.eeeeeeee...eeeeeeee..eeeeeeee.eeeeeee....eeeeeee..eeeee.....eeeee......eeeeeeee.........eee........hhhhhhhhhhhhhhhh.hhhhhhhhhh.......eee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dgr B  46 NNPYLFRSNKFLTLFKNQHGSLRLLQRFNEDTEKLENLRDYRVLEYCSKPNTLLLPHHSDSDLLVLVLEGQAILVLVNPDGRDTYKLDQGDAIKIQAGTPFYLINPDNNQNLRILKFAITFRRPGTVEDFFLSSTKRLPSYLSAFSKNFLEASYDSPYDEIEQTLLQEEQEGVIVKMP 223
                                    55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215        


Chain C from PDB  Type:PROTEIN  Length:178
 aligned with CANA_CANEN | P50477 from UniProtKB/Swiss-Prot  Length:445

    Alignment length:178
                                    55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215        
           CANA_CANEN    46 NNPYLFRSNKFLTLFKNQHGSLRLLQRFNEDTEKLENLRDYRVLEYCSKPNTLLLPHHSDSDLLVLVLEGQAILVLVNPDGRDTYKLDQGDAIKIQAGTPFYLINPDNNQNLRILKFAITFRRPGTVEDFFLSSTKRLPSYLSAFSKNFLEASYDSPYDEIEQTLLQEEQEGVIVKMP 223
               SCOP domains d1dgrc_ C: Seed storage 7S protein                                                                                                                                                 SCOP domains
               CATH domains 1dgrC00 C:46-223 Jelly Rolls                                                                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eehhh.eeeeeee..eeeeee......hhhhhhhh.eeeeeeee...eeeeeeee..eeeeeeee.eeeeeee....eeeeeee..eeeee.....eeeee......eeeeeeee.........eee........hhhhhhhhhhhhhhhh.hhhhhhhhhh.......eee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dgr C  46 NNPYLFRSNKFLTLFKNQHGSLRLLQRFNEDTEKLENLRDYRVLEYCSKPNTLLLPHHSDSDLLVLVLEGQAILVLVNPDGRDTYKLDQGDAIKIQAGTPFYLINPDNNQNLRILKFAITFRRPGTVEDFFLSSTKRLPSYLSAFSKNFLEASYDSPYDEIEQTLLQEEQEGVIVKMP 223
                                    55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215        


Chain M from PDB  Type:PROTEIN  Length:92
 aligned with CANA_CANEN | P50477 from UniProtKB/Swiss-Prot  Length:445

    Alignment length:92
                                   341       351       361       371       381       391       401       411       421  
           CANA_CANEN   332 QLRRYAATLSEGDIIVIPSSFPVALKAASDLNMVGIGVNAENNERNFLAGHKENVIRQIPRQVSDLTFPGSGEEVEELLENQKESYFVDGQP 423
               SCOP domains d1dgr.4 N:,M: Seed storage 7S protein                                                        SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee....eeee.....eeeee...eeeeeeee......eee.......hhhhhhhhhhhhhh..hhhhhhhhh.......eee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                 1dgr M 332 QLRRYAATLSEGDIIVIPSSFPVALKAASDLNMVGIGVNAENNERNFLAGHKENVIRQIPRQVSDLTFPGSGEEVEELLENQKESYFVDGQP 423
                                   341       351       361       371       381       391       401       411       421  


Chain N from PDB  Type:PROTEIN  Length:76
 aligned with CANA_CANEN | P50477 from UniProtKB/Swiss-Prot  Length:445

    Alignment length:76
                                   255       265       275       285       295       305       315      
           CANA_CANEN   246 DKPFNLRSRDPIYSNNYGKLYEITPEKNSQLRDLDILLNCLQMNEGALFVPHYNSRATVILVANEGRAEVELVGLE 321
               SCOP domains d1dgr.4 N:,M: Seed storage 7S protein                                        SCOP domains
               CATH domains ---------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.......ee...eeeeee....hhhhhhhh.eeeeeee...eeeeeeee...eeeeeeee..eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------- Transcript
                 1dgr N 246 DKPFNLRSRDPIYSNNYGKLYEITPEKNSQLRDLDILLNCLQMNEGALFVPHYNSRATVILVANEGRAEVELVGLE 321
                                   255       265       275       285       295       305       315      


Chain V from PDB  Type:PROTEIN  Length:76
 aligned with CANA_CANEN | P50477 from UniProtKB/Swiss-Prot  Length:445

    Alignment length:76
                                   255       265       275       285       295       305       315      
           CANA_CANEN   246 DKPFNLRSRDPIYSNNYGKLYEITPEKNSQLRDLDILLNCLQMNEGALFVPHYNSRATVILVANEGRAEVELVGLE 321
               SCOP domains d1dgr.2 V:,W: Seed storage 7S protein                                        SCOP domains
               CATH domains ---------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.......ee...eeeeee....hhhhhhhheeeeeeee...eeeeeeee...eeeeeeee..eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------- Transcript
                 1dgr V 246 DKPFNLRSRDPIYSNNYGKLYEITPEKNSQLRDLDILLNCLQMNEGALFVPHYNSRATVILVANEGRAEVELVGLE 321
                                   255       265       275       285       295       305       315      


Chain W from PDB  Type:PROTEIN  Length:93
 aligned with CANA_CANEN | P50477 from UniProtKB/Swiss-Prot  Length:445

    Alignment length:93
                                   340       350       360       370       380       390       400       410       420   
           CANA_CANEN   331 MQLRRYAATLSEGDIIVIPSSFPVALKAASDLNMVGIGVNAENNERNFLAGHKENVIRQIPRQVSDLTFPGSGEEVEELLENQKESYFVDGQP 423
               SCOP domains d1dgr.2 V:,W: Seed storage 7S protein                                                         SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee....eeee.....eeeee...eeeeeeee......eee.......hhhhhhhhhhhhhh..hhhhhhhhh.......eee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 1dgr W 331 MQLRRYAATLSEGDIIVIPSSFPVALKAASDLNMVGIGVNAENNERNFLAGHKENVIRQIPRQVSDLTFPGSGEEVEELLENQKESYFVDGQP 423
                                   340       350       360       370       380       390       400       410       420   


Chain X from PDB  Type:PROTEIN  Length:75
 aligned with CANA_CANEN | P50477 from UniProtKB/Swiss-Prot  Length:445

    Alignment length:75
                                   255       265       275       285       295       305       315     
           CANA_CANEN   246 DKPFNLRSRDPIYSNNYGKLYEITPEKNSQLRDLDILLNCLQMNEGALFVPHYNSRATVILVANEGRAEVELVGL 320
               SCOP domains d1dgr.1 X:,Y: Seed storage 7S protein                                       SCOP domains
               CATH domains --------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.......ee...eeeeee....hhhhhhhheeeeeeee...eeeeeeee...eeeeeeee..eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                 1dgr X 246 DKPFNLRSRDPIYSNNYGKLYEITPEKNSQLRDLDILLNCLQMNEGALFVPHYNSRATVILVANEGRAEVELVGL 320
                                   255       265       275       285       295       305       315     


Chain Y from PDB  Type:PROTEIN  Length:93
 aligned with CANA_CANEN | P50477 from UniProtKB/Swiss-Prot  Length:445

    Alignment length:93
                                   340       350       360       370       380       390       400       410       420   
           CANA_CANEN   331 MQLRRYAATLSEGDIIVIPSSFPVALKAASDLNMVGIGVNAENNERNFLAGHKENVIRQIPRQVSDLTFPGSGEEVEELLENQKESYFVDGQP 423
               SCOP domains d1dgr.1 X:,Y: Seed storage 7S protein                                                         SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee....eeee.....eeeee...eeeeeeee......eee.......hhhhhhhhhhhhhh..hhhhhhhhh.......eee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 1dgr Y 331 MQLRRYAATLSEGDIIVIPSSFPVALKAASDLNMVGIGVNAENNERNFLAGHKENVIRQIPRQVSDLTFPGSGEEVEELLENQKESYFVDGQP 423
                                   340       350       360       370       380       390       400       410       420
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 6)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1DGR)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,M,N,V,W,X,Y   (CANA_CANEN | P50477)
molecular function
    GO:0045735    nutrient reservoir activity    Functions in the storage of nutritious substrates.

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  1dgr
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  CANA_CANEN | P50477
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        CANA_CANEN | P50477: 1cau 1cav 1caw 1cax 1dgw 2cau 2cav

(-) Related Entries Specified in the PDB File

1caw EARLIER VERSION OF ORTHORHOMBIC FORM OF CANAVALIN
1cax EARLIER VERSION OF RHOMBOHEDRAL FORM OF CANAVALIN
1dgw ORTHORHOMBIC FORM OF CANAVALIN
2cau CUBIC FORM OF CANAVALIN
2cav HEXAGONAL FORM OF CANAVALIN